Nowak works on the dynamics of infectious diseases, cancer genetics, the evolution of cooperation and human language. His first book, Virus Dynamics (written with Robert May) was published by Oxford University Press, 2000. Nowak is a corresponding member of the Austrian academy of sciences. He won the Weldon Memorial Prize, the Albert Wander Prize, the Akira Okubo Prize, the David Starr Jordan Prize[9] and the Henry Dale Prize. His 2006 book Evolutionary Dynamics: Exploring the Equations of Life[10] was published in 2006 to critical acclaim[11] and won the Association of American Publishers R.R. Hawkins Award for the Outstanding Professional, Reference or Scholarly Work of 2006.[12]

Nowak was co-director with Sarah Coakley of the Evolution and Theology of Cooperation project at Harvard University, sponsored by the Templeton Foundation.[13] He is also a member of the Board of Advisers of the Templeton Foundation.[14] In a lecture given at Harvard in March 2007 called "Evolution and Christianity", Nowak, a Roman Catholic,[15] argued that "Science and religion are two essential components in the search for truth. Denying either is a barren approach."[16]

He has over 300 scientific publications, of which 40 are in Nature and 15 in Science.[17]

In 2010 a paper by Nowak, EO Wilson, and Corina Tarnita, in Nature, argued that standard natural selection theory represents a simpler and superior approach to kin selection theory in the evolution of eusociality.[18] This work has led to many comments including strong criticism from proponents of inclusive fitness theory.[19][20][21][22] Nowak maintains that the findings of the paper are conclusive and that the field of social evolution should move beyond the limitations imposed by inclusive fitness theory.[23][24]

In 2011 his book Supercooperators: The Mathematics of Evolution, Altruism and Human Behaviour (Or, Why We Need Each Other to Succeed) was published, co-authored with Roger Highfield.

Manfred Milinski in Nature describes the book as "part autobiography, part textbook, and reads like a best-selling novel" and suggests that whereas Nowak is right that the theories of kin selection and punishment need revisiting, it is too soon to tell whether his bold ideas will hold up to empirical testing. On the Nowak/Tarnita/Wilson paper Milinski says: "I anticipate that a better mathematical formulation of social evolution theory will be found that includes relatedness, is compatible with existing evidence and includes Hamilton's rule as a rule of thumb."[25]

David Willetts, in the Financial Times, described the book as an "excellent example" of using the nexus of evolutionary biology, game theory and neuroscience to understand the development of cooperation in society, and suggests that "all politicians can draw inspiration and ideas from the intellectual resources of this exciting approach"[26]

In 1990 Nowak and Robert May proposed a mathematical model which explained the puzzling delay between HIV infection and AIDS in terms of the evolution of different strains of the virus during individual infections, to the point where the genetic diversity of the virus reaches a threshold whereby the immune system can no longer control it.[27]
This detailed quantitative approach depended on assumptions about the biology of HIV which were subsequently confirmed by experiment.[28]

In a paper in Science in 2006 Nowak enunciated and unified the mathematical rules for the five understood bases of the evolution of cooperation (kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection). Nowak suggests that evolution is constructive because of cooperation, and that we might add “natural cooperation” as a third fundamental principle of evolution beside mutation and natural selection.[29]

In a paper featured on the front cover of Nature Nowak and colleagues demonstrated that the transition of irregular verbs to regular verbs in English over time obeys a simple inverse-square law, thus providing one of the first quantitative laws in the evolution of language.[30]

1998-2003 Head, Program in Theoretical Biology Institute for Advanced Study. From 1999-2003 he was Associated Faculty, Ecology and Evolutionary Biology and from 2000-2003 also Associated Faculty, Program in Applied and Computational Mathematics

^e.g. in Nature "It should be on the shelf of anyone who has, or thinks they might have, an interest in theoretical biology" " wonderfully well-presented, and offers a new range of insights into interesting and important and emerging topics in mathematical biology." Robert May. ""rigor and new ideas into the study of the evolution of language and cooperation...brimming with insights and surprising findings and should be of interest to anyone who is curious about these topics" Steven Pinker "A brilliant book by a master of his field" Robert Trivers "a remarkable book, absolutely original, containing a lot of material which has never before appeared in book form. It is written in a very accessible style, and leads almost effortlessly from first principles to state-of-the-art research. The book takes an eagle's view on evolution, covering a vast range of topics from molecules to man. It emphasises analytical methods and presents a large canvas of superbly elegant mathematical models." Karl Sigmund